G1
>Silph Co.http://www.youtube.com/watch?v=NgXI10XEY5E (8-Bit doesn't really do it justice, but one felt like potentially the most ingenious of G1).
>Trainer Battlehttp://www.youtube.com/watch?v=z2Nr8na3pf4 It's more 'not bad' than good, but it's still neat along with the gym leader.
G2:
>Champion Battle - Lance & RedI don't even need link this one because it's popular burned into most peoples' permanent memory and/or already mentioned.
>Violet Cityhttp://www.youtube.com/watch?v=kFNHlJ6yvEA - I just like it.
>Slowpoke Well/Ice Path/Dark Cavehttp://www.youtube.com/watch?v=kchmJhxwr_E - just memorable
G3
>Route 113http://www.youtube.com/watch?v=gHYUD3oDXbM Something bugged me about the music theory & the GBA soundchips for Gen 3, but this one stood out on all accounts.
Gen 4
>Coronet Peakhttp://www.youtube.com/watch?v=M-GFxbkGmMQ - Gen 4 brought some intense atmospheric themes to the franchise; this one being one of them.
>Eterna Foresthttp://www.youtube.com/watch?v=uBKJdlFLtFU The kind of song that makes you just want to stay where you are.
Gen 5:
>Sekka Cityhttp://www.youtube.com/watch?v=x7d3ncU9aIk >Team Plasma Grunthttp://www.youtube.com/watch?v=cp3FtEaV7tQ>Dragonspiral Towerhttp://www.youtube.com/watch?v=s-ty6u4RxWI - all of these songs are very similar to Chrono Trigger and Zelda LttP, but that's not necessarily a bad thing.
Other:
>Miror B http://www.youtube.com/watch?v=kAHHFc-gIeI hands down most creative Pokemon villain theme ever.
>Petit Cup Finalehttp://www.youtube.com/watch?v=M06UDidri5E - One may have been forgotten.
>Ronald's Themehttp://www.youtube.com/watch?v=al1TH4WOYCM - The era when the cards were all the rage.
>Sky Tower & Primal Dialgahttp://www.youtube.com/watch?v=tKMWMS7O50ghttp://www.youtube.com/watch?v=9D8FkBgKOK8 Two pieces of the Mystery Dungeon Master Race
Honorable Mention:
>Dullahan Under the Willowshttp://www.youtube.com/watch?v=O3ZfPNmXpyg only here for having similar core Pokemon traits.